Preheat oven to 350 degrees F. In large bowl, combine navy beans, red bell pepper, and red onion. In separate bowl, whisk together all remaining ingredients. Pour sauce over navy bean mixture and stir until beans are coated evenly.
Transfer mixture to a 9x13-inch baking dish and bake for 45 to 50 minutes, or until beans are hot and bubbly. Let cool a few minutes before serving.